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You can ignore the warning. There's an attempt to build module dependencies (although the reason for this is not clear, and might be worth investigating), and the message says there's no deployed module for the one you've been generating (which it's true for the transient module of generated models), and that we use module source to find out its dependencies.

If the message show up during transformation/text generation, removing the module won't help. If it happens afterwards, you can avoid the message by disposing the transient module - right click in project pane, 'Remove transients' action.

Yes, this is what I currently do (right click, dispose). The message does not show up automatically, only when I open the transient. Is there a way to dispose the transient automatically and not requiring the user to dispose it manually?